Stacking-unstacking dynamics of oligodeoxynucleotide trimers

John M. Jean, Kathleen B. Hall

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

The structure and dynamics of DNA trimers are experimentally assessed using the fluorescent purine analogue 2-aminopurine (2AP), incorporating 2AP between purine and pyrimidine bases to form 5′dXp2APpY 3′ molecules. Circular dichroism and fluorescence quenching of the 2AP show that the bases are stacked; at the same time, fluorescence decay lifetimes are heterogeneous, indicative of conformational sampling. 2AP does not exhibit the long fluorescence decay time characteristic of the free nucleoside, suggesting that its motions in the trimers bring it into proximity of the neighboring bases, resulting in efficient charge transfer and average fluorescence lifetimes on the order of 1-2 ns.

Original languageEnglish
Pages (from-to)10277-10284
Number of pages8
JournalBiochemistry
Volume43
Issue number31
DOIs
StatePublished - Aug 10 2004

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